Rendered image/video loses material and lighting
Managed to find the issue.

Under the render layers tab, there is a material override option, that replaces all materials with only one. My issue was fixed when clearing this material option.



EDIT:

Newer versions of blender don't use layers, but "collections" so the override function is in the scene>View Layer section.



Additional info:

Where is the Layers panel in Blender 2.8?

2.8 - Is it possible to assign (override) a material to a whole collection?